ExtendedNewick.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_IO_EXTENDEDNEWICK_H
#define BPP_PHYL_IO_EXTENDEDNEWICK_H
 
 
#include "../Tree/PhyloDAG.h"
#include "IoDAG.h"
 
namespace bpp
{
class ExtendedNewick :
  public AbstractIPhyloDAG,
  public AbstractOPhyloDAG,
  public AbstractIMultiPhyloDAG,
  public AbstractOMultiPhyloDAG
{
protected:
  bool allowComments_;
  bool writeId_;
  bool verbose_;
 
public:
  ExtendedNewick(bool allowComments = false, bool writeId = false, bool verbose = false) :
    allowComments_(allowComments),
    writeId_(writeId),
    verbose_(verbose)
  {}
 
  virtual ~ExtendedNewick() {}
 
public:
  const std::string getFormatName() const override;
  const std::string getFormatDescription() const override;
  /* @} */
 
  using AbstractIPhyloDAG::readPhyloDAG;
 
  std::unique_ptr<PhyloDAG> readPhyloDAG(std::istream& in) const override;
 
private:
  std::shared_ptr<PhyloNode> parenthesisToNode(
      PhyloDAG& dag,
      std::shared_ptr<PhyloNode> father,
      const std::string& description,
      unsigned int& nodeCounter,
      unsigned int& branchCounter,
      std::map<std::string, std::shared_ptr<PhyloNode>>& mapEvent,
      bool withId,
      bool verbose) const;
 
public:
  std::unique_ptr<PhyloDAG> parenthesisToPhyloDAG(
      const std::string& description,
      bool withId,
      bool verbose = false) const;
 
public:
  using AbstractOPhyloDAG::writePhyloDAG;
 
  void writePhyloDAG(const PhyloDAG& dag, std::ostream& out) const override
  {
    write_(dag, out);
  }
  using AbstractIMultiPhyloDAG::readPhyloDAGs;
 
  void readPhyloDAGs(
      std::istream& in,
      std::vector<std::unique_ptr<PhyloDAG>>& dags) const override;
 
  using AbstractOMultiPhyloDAG::writePhyloDAGs;
 
  void writePhyloDAGs(const std::vector<const PhyloDAG*>& dags, std::ostream& out) const override
  {
    write_(dags, out);
  }
protected:
  void write_(const PhyloDAG& tree, std::ostream& out) const;
 
  void write_(const std::vector<const PhyloDAG*>& dags, std::ostream& out) const;
 
  Element getElement(const std::string& elt) const override;
 
  std::string edgeToParenthesis(const PhyloDAG& dag, std::shared_ptr<PhyloBranch> edge, std::vector<std::shared_ptr<PhyloNode>>& writtenNodes, bool writeId = false) const;
 
  std::string dagToParenthesis(const PhyloDAG& dag, bool writeId = false) const;
};
} // end of namespace bpp.
#endif // BPP_PHYL_IO_EXTENDEDNEWICK_H